Introduction

Analysis of MCF10A in 16 different conditions 2 biological replicates per sample

This report was made following John’s suggestion to check the difference between the samples separated by PC1.

Create new coldata

Add to the metadata to group the PC1 left group (EGF Oligo and growth medium) vs all other samples.

PCA

All conditions

Heatmap of z score

Comparing the EGF+Oligo vs all others (excluding GM)

x
Intercept
PC1_OlEGF_vs_others
PC1_out_vs_others
replicate

Volcano plots

GSEA analysis (logFc)

GOBP

GOMF

Reactome

KEGG

Wikipathways

What effects comes from EGF and what comes oligo?

## [1] "Intercept"               "PC1_sep_EGF_vs_others"  
## [3] "PC1_sep_Oligo_vs_others" "PC1_sep_out_vs_others"  
## [5] "replicate"

Venn diagram of common genes

But this doesn’t take into account the logFc of the change in those genes Is there a way to score a pathway such as: - EGF explains 20% of the change in that pathway’s enrichment - Oligo explains the other 80%

GSEA

GOBP

Get the common terms and facet grid the different comparisons

Reactome

Get the common terms and facet grid the different comparisons

## R version 4.2.2 (2022-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
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## Matrix products: default
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## locale:
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## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.utf8    
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
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## other attached packages:
##  [1] lubridate_1.9.0             timechange_0.1.1           
##  [3] ReactomePA_1.42.0           org.Hs.eg.db_3.16.0        
##  [5] AnnotationDbi_1.60.0        NMF_0.26                   
##  [7] cluster_2.1.4               rngtools_1.5.2             
##  [9] registry_0.5-1              clusterProfiler_4.6.0      
## [11] msigdbr_7.5.1               xlsx_0.6.5                 
## [13] pheatmap_1.0.12             ggrepel_0.9.2              
## [15] biomaRt_2.54.1              cowplot_1.1.1              
## [17] DESeq2_1.38.1               SummarizedExperiment_1.28.0
## [19] Biobase_2.58.0              MatrixGenerics_1.10.0      
## [21] matrixStats_0.62.0          GenomicRanges_1.49.0       
## [23] GenomeInfoDb_1.34.4         IRanges_2.32.0             
## [25] S4Vectors_0.36.0            BiocGenerics_0.44.0        
## [27] forcats_0.5.2               stringr_1.4.1              
## [29] dplyr_1.0.10                purrr_0.3.5                
## [31] readr_2.1.3                 tidyr_1.2.1                
## [33] tibble_3.1.8                ggplot2_3.4.0              
## [35] tidyverse_1.3.2             RColorBrewer_1.1-3         
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.2             tidyselect_1.2.0       RSQLite_2.2.19        
##   [4] grid_4.2.2             BiocParallel_1.32.4    scatterpie_0.1.8      
##   [7] munsell_0.5.0          codetools_0.2-18       withr_2.5.0           
##  [10] colorspace_2.0-3       GOSemSim_2.24.0        filelock_1.0.2        
##  [13] highr_0.9              knitr_1.41             rstudioapi_0.14       
##  [16] rJava_1.0-6            DOSE_3.24.2            labeling_0.4.2        
##  [19] GenomeInfoDbData_1.2.9 polyclip_1.10-4        bit64_4.0.5           
##  [22] farver_2.1.1           downloader_0.4         vctrs_0.5.0           
##  [25] treeio_1.22.0          generics_0.1.3         gson_0.0.9            
##  [28] xfun_0.34              BiocFileCache_2.6.1    R6_2.5.1              
##  [31] doParallel_1.0.17      graphlayouts_0.8.4     locfit_1.5-9.6        
##  [34] bitops_1.0-7           cachem_1.0.6           fgsea_1.24.0          
##  [37] gridGraphics_0.5-1     DelayedArray_0.23.2    assertthat_0.2.1      
##  [40] scales_1.2.1           ggraph_2.1.0           enrichplot_1.18.3     
##  [43] googlesheets4_1.0.1    gtable_0.3.1           tidygraph_1.2.2       
##  [46] rlang_1.0.6            splines_4.2.2          lazyeval_0.2.2        
##  [49] gargle_1.2.1           broom_1.0.1            BiocManager_1.30.19   
##  [52] yaml_2.3.6             reshape2_1.4.4         modelr_0.1.10         
##  [55] backports_1.4.1        qvalue_2.30.0          tools_4.2.2           
##  [58] ggplotify_0.1.0        gridBase_0.4-7         ellipsis_0.3.2        
##  [61] jquerylib_0.1.4        Rcpp_1.0.9             plyr_1.8.8            
##  [64] progress_1.2.2         zlibbioc_1.44.0        RCurl_1.98-1.9        
##  [67] prettyunits_1.1.1      viridis_0.6.2          haven_2.5.2           
##  [70] fs_1.5.2               magrittr_2.0.3         data.table_1.14.4     
##  [73] reactome.db_1.82.0     reprex_2.0.2           googledrive_2.0.0     
##  [76] hms_1.1.2              xlsxjars_0.6.1         patchwork_1.1.2       
##  [79] evaluate_0.18          xtable_1.8-4           HDO.db_0.99.1         
##  [82] XML_3.99-0.13          readxl_1.4.1           gridExtra_2.3         
##  [85] compiler_4.2.2         crayon_1.5.2           shadowtext_0.1.2      
##  [88] htmltools_0.5.3        ggfun_0.0.9            tzdb_0.3.0            
##  [91] snow_0.4-4             geneplotter_1.76.0     aplot_0.1.9           
##  [94] DBI_1.1.3              tweenr_2.0.2           dbplyr_2.2.1          
##  [97] MASS_7.3-58.1          rappdirs_0.3.3         babelgene_22.9        
## [100] Matrix_1.5-1           cli_3.4.1              parallel_4.2.2        
## [103] igraph_1.3.5           pkgconfig_2.0.3        xml2_1.3.3            
## [106] foreach_1.5.2          ggtree_3.6.2           annotate_1.76.0       
## [109] bslib_0.4.1            XVector_0.38.0         rvest_1.0.3           
## [112] yulab.utils_0.0.6      digest_0.6.30          graph_1.76.0          
## [115] Biostrings_2.66.0      rmarkdown_2.18         cellranger_1.1.0      
## [118] fastmatch_1.1-3        tidytree_0.4.2         curl_4.3.3            
## [121] graphite_1.44.0        lifecycle_1.0.3        nlme_3.1-160          
## [124] jsonlite_1.8.3         viridisLite_0.4.1      fansi_1.0.3           
## [127] pillar_1.8.1           lattice_0.20-45        KEGGREST_1.38.0       
## [130] fastmap_1.1.0          httr_1.4.4             GO.db_3.16.0          
## [133] glue_1.6.2             png_0.1-7              iterators_1.0.14      
## [136] bit_4.0.4              ggforce_0.4.1          stringi_1.7.8         
## [139] sass_0.4.2             blob_1.2.3             memoise_2.0.1         
## [142] ape_5.6-2